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java.lang.Objectuk.ac.sanger.psu.gfmerge.datacomp.GFMergeFeature
public abstract class GFMergeFeature
abstract class which contains basic implementation of genemodels, blast and cDNA features.
GeneModel
,
SimFeature
Field Summary | |
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private java.util.ArrayList |
exons
ArrayList of exon within a genemodel |
private org.biojava.bio.seq.StrandedFeature |
feature
BioJava feature object |
private java.util.ArrayList |
introns
ArrayList of introns within a genemodel |
Constructor Summary | |
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GFMergeFeature(org.biojava.bio.seq.StrandedFeature feature)
constructor which contains basic implementation for GeneModel and SimFeature objects |
Method Summary | |
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java.util.ArrayList |
getExons()
accessor method which returns ArrayList of exons |
org.biojava.bio.seq.StrandedFeature |
getFeature()
accessor method which returns the appertaining StrandedFeature retrieved from file |
java.util.ArrayList |
getIntrons()
accessor method which returns ArrayList of introns |
long |
getLength()
accessor method which returns the length of the feature |
org.biojava.bio.symbol.Location |
getLocation()
accessor method which returns Location of the BioJava feature |
org.biojava.bio.seq.StrandedFeature.Strand |
getStrand()
accessor method which returns Strand of the BioJava feature |
long |
getTotalExonLength()
accessor method which returns total exon length of the feature |
private void |
setExons(org.biojava.bio.seq.Feature _feature)
accessor method which calculates exons of feature. |
private void |
setFeature(org.biojava.bio.seq.StrandedFeature _feature)
accessor method which sets BioJava feature |
private void |
setIntrons(org.biojava.bio.seq.Feature _feature)
accessor method which calculates introns of feature. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private org.biojava.bio.seq.StrandedFeature feature
private java.util.ArrayList exons
private java.util.ArrayList introns
Constructor Detail |
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public GFMergeFeature(org.biojava.bio.seq.StrandedFeature feature)
feature
- BioJava featureMethod Detail |
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public org.biojava.bio.seq.StrandedFeature getFeature()
getFeature
in interface GFMergeFeatureAble
public java.util.ArrayList getExons()
getExons
in interface GFMergeFeatureAble
public java.util.ArrayList getIntrons()
getIntrons
in interface GFMergeFeatureAble
public org.biojava.bio.symbol.Location getLocation()
getLocation
in interface LocateAble
public org.biojava.bio.seq.StrandedFeature.Strand getStrand()
public long getLength()
getLength
in interface GFMergeFeatureAble
public long getTotalExonLength()
getTotalExonLength
in interface GFMergeFeatureAble
TotalExonLengthAnalysis
private void setFeature(org.biojava.bio.seq.StrandedFeature _feature)
_feature
- BioJava featureprivate void setExons(org.biojava.bio.seq.Feature _feature)
_feature
- BioJava featureprivate void setIntrons(org.biojava.bio.seq.Feature _feature)
_feature
- BioJava feature
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